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cgpCaVEManPostProcessing

DOI

cgpCaVEManPostProcessing is used to apply filtering on raw VCF calls generated using CaVEMan.

For details of the underlying algorithm please see the CaVEMan site.

Master Develop
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Docker, Singularity and Dockstore

There are pre-built images containing this codebase on quay.io.

These were primarily designed for use with dockstore.org but can be used as normal containers.

Dependencies/Install

Please install the following first:

Please see these for any child dependencies.

Once complete please run:

./setup.sh /some/install/location

setup.sh will also install bedtools for you.

Creating a release

Preparation

  • Commit/push all relevant changes.
  • Pull a clean version of the repo and use this for the following steps.

Cutting the release

  1. Update perl/lib/Sanger/CGP/CavemanPostProcessor.pm to the correct version.
  2. Run ./prerelease.sh
  3. Check all tests and coverage reports are acceptable.
  4. Commit the updated docs tree and updated module/version.
  5. Push commits.
  6. Use the GitHub tools to draft a release.

LICENCE

Copyright (c) 2014-2018 Genome Research Ltd.

Author: CASM/Cancer IT <[email protected]>

This file is part of cgpCaVEManPostProcessing.

cgpCaVEManPostProcessing is free software: you can redistribute it and/or modify it under
the terms of the GNU Affero General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option) any
later version.

This program is distributed in the hope that it will be useful, but WITHOUT
ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more
details.

You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.

1. The usage of a range of years within a copyright statement contained within
this distribution should be interpreted as being equivalent to a list of years
including the first and last year specified and all consecutive years between
them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007-
2009, 2011-2012’ should be interpreted as being identical to a statement that
reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright
statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being
identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008,
2009, 2010, 2011, 2012’."